Starting phenix.real_space_refine on Sun May 18 23:41:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmb_41383/05_2025/8tmb_41383.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 59 5.16 5 C 10556 2.51 5 N 2639 2.21 5 O 2969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16229 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2830 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2917 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.99, per 1000 atoms: 0.62 Number of scatterers: 16229 At special positions: 0 Unit cell: (113.3, 139.05, 167.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 Mg 6 11.99 O 2969 8.00 N 2639 7.00 C 10556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.1 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 51.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.563A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.684A pdb=" N LYS A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.805A pdb=" N TYR A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 4.067A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.774A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 302 removed outlier: 3.671A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 325 through 347 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.206A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 80 removed outlier: 4.090A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.508A pdb=" N LEU B 87 " --> pdb=" O HIS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 165 through 202 Processing helix chain 'B' and resid 205 through 238 removed outlier: 3.897A pdb=" N GLN B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.611A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 311 removed outlier: 4.148A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.975A pdb=" N LYS B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.363A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.764A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.627A pdb=" N LEU C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 165 through 201 Processing helix chain 'C' and resid 206 through 238 removed outlier: 3.912A pdb=" N THR C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.144A pdb=" N TYR C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 298 removed outlier: 3.832A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.687A pdb=" N ILE C 307 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 345 removed outlier: 3.958A pdb=" N VAL C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.530A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix removed outlier: 3.604A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.555A pdb=" N LYS D 164 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.528A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 238 removed outlier: 4.052A pdb=" N ARG D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 4.250A pdb=" N ASP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.546A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 327 through 349 removed outlier: 4.496A pdb=" N VAL D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.613A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 Processing helix chain 'E' and resid 205 through 237 removed outlier: 4.152A pdb=" N GLN E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.947A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 298 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 330 through 348 Processing helix chain 'H' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 3.786A pdb=" N GLU B 28 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.058A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 removed outlier: 7.110A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 44 removed outlier: 6.800A pdb=" N THR E 60 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET E 138 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE E 62 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN E 140 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 64 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.619A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.426A pdb=" N GLY H 13 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.426A pdb=" N GLY H 13 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR H 122 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE H 103 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N MET H 120 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 106 through 107 removed outlier: 3.709A pdb=" N TYR H 114 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.781A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.579A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA L 14 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.522A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5076 1.34 - 1.46: 3235 1.46 - 1.58: 8178 1.58 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 16598 Sorted by residual: bond pdb=" CA ARG D 202 " pdb=" CB ARG D 202 " ideal model delta sigma weight residual 1.525 1.539 -0.015 8.30e-03 1.45e+04 3.09e+00 bond pdb=" C TYR E 327 " pdb=" N PRO E 328 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.32e+00 bond pdb=" CB PRO L 45 " pdb=" CG PRO L 45 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CA TYR D 327 " pdb=" C TYR D 327 " ideal model delta sigma weight residual 1.532 1.523 0.009 6.50e-03 2.37e+04 1.78e+00 bond pdb=" C ASP A 148 " pdb=" N PRO A 149 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.55e+00 ... (remaining 16593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 22212 2.71 - 5.41: 266 5.41 - 8.12: 25 8.12 - 10.82: 1 10.82 - 13.53: 1 Bond angle restraints: 22505 Sorted by residual: angle pdb=" C LEU C 321 " pdb=" CA LEU C 321 " pdb=" CB LEU C 321 " ideal model delta sigma weight residual 117.23 111.19 6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" C LEU D 235 " pdb=" N TYR D 236 " pdb=" CA TYR D 236 " ideal model delta sigma weight residual 122.09 114.78 7.31 1.79e+00 3.12e-01 1.67e+01 angle pdb=" N VAL D 290 " pdb=" CA VAL D 290 " pdb=" C VAL D 290 " ideal model delta sigma weight residual 110.42 106.58 3.84 9.60e-01 1.09e+00 1.60e+01 angle pdb=" N VAL A 93 " pdb=" CA VAL A 93 " pdb=" C VAL A 93 " ideal model delta sigma weight residual 112.17 108.40 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.53 114.94 7.59 1.92e+00 2.71e-01 1.56e+01 ... (remaining 22500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8887 17.94 - 35.87: 888 35.87 - 53.81: 164 53.81 - 71.74: 27 71.74 - 89.68: 17 Dihedral angle restraints: 9983 sinusoidal: 4164 harmonic: 5819 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 39.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N ALA A 308 " pdb=" CA ALA A 308 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE B 315 " pdb=" C PHE B 315 " pdb=" N GLU B 316 " pdb=" CA GLU B 316 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 9980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1902 0.048 - 0.096: 527 0.096 - 0.145: 112 0.145 - 0.193: 9 0.193 - 0.241: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" C PRO L 45 " pdb=" CB PRO L 45 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU A 304 " pdb=" CB LEU A 304 " pdb=" CD1 LEU A 304 " pdb=" CD2 LEU A 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE D 296 " pdb=" CA ILE D 296 " pdb=" CG1 ILE D 296 " pdb=" CG2 ILE D 296 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2548 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 44 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO L 45 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 306 " -0.028 2.00e-02 2.50e+03 2.28e-02 9.10e+00 pdb=" CG PHE E 306 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE E 306 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 306 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 306 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 306 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO L 9 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " -0.030 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 201 2.66 - 3.22: 16161 3.22 - 3.78: 25581 3.78 - 4.34: 34069 4.34 - 4.90: 55918 Nonbonded interactions: 131930 Sorted by model distance: nonbonded pdb=" OE1 GLU D 186 " pdb=" OG SER E 7 " model vdw 2.100 3.040 nonbonded pdb=" O THR C 295 " pdb=" OG1 THR C 299 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 43 " model vdw 2.164 3.120 nonbonded pdb=" ND2 ASN B 314 " pdb=" OD1 ASN C 314 " model vdw 2.201 3.120 nonbonded pdb=" OG SER A 35 " pdb=" O GLU A 38 " model vdw 2.216 3.040 ... (remaining 131925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 351) selection = (chain 'B' and resid 17 through 351) selection = (chain 'C' and resid 17 through 351) selection = (chain 'D' and resid 17 through 351) selection = (chain 'E' and resid 17 through 351) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.770 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16600 Z= 0.166 Angle : 0.706 13.530 22509 Z= 0.378 Chirality : 0.045 0.241 2551 Planarity : 0.006 0.112 2816 Dihedral : 14.696 89.679 6219 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.39 % Favored : 94.25 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1947 helix: 1.22 (0.17), residues: 929 sheet: -0.66 (0.28), residues: 345 loop : -2.09 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 350 HIS 0.004 0.001 HIS C 212 PHE 0.052 0.002 PHE E 306 TYR 0.023 0.001 TYR A 236 ARG 0.015 0.001 ARG C 5 Details of bonding type rmsd hydrogen bonds : bond 0.13366 ( 945) hydrogen bonds : angle 6.33738 ( 2727) SS BOND : bond 0.00541 ( 2) SS BOND : angle 1.23855 ( 4) covalent geometry : bond 0.00372 (16598) covalent geometry : angle 0.70552 (22505) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 1.815 Fit side-chains REVERT: A 100 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 174 ILE cc_start: 0.8583 (mm) cc_final: 0.8382 (mm) REVERT: A 186 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5783 (mm-30) REVERT: A 286 LYS cc_start: 0.7954 (tptt) cc_final: 0.7091 (tmtt) REVERT: A 317 TYR cc_start: 0.5759 (t80) cc_final: 0.5398 (t80) REVERT: A 334 MET cc_start: 0.5044 (mmp) cc_final: 0.4813 (tpp) REVERT: B 96 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7468 (ttm170) REVERT: B 155 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7027 (tpp80) REVERT: B 186 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 197 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6552 (mm-30) REVERT: B 313 MET cc_start: 0.5462 (mtp) cc_final: 0.5132 (mtp) REVERT: B 318 MET cc_start: 0.0792 (tpt) cc_final: -0.0651 (tpt) REVERT: C 22 LYS cc_start: 0.7524 (pttm) cc_final: 0.7301 (pttm) REVERT: C 35 SER cc_start: 0.8753 (t) cc_final: 0.8422 (t) REVERT: D 23 TYR cc_start: 0.7675 (m-10) cc_final: 0.7364 (m-80) REVERT: D 163 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7887 (mtmt) REVERT: D 318 MET cc_start: 0.5639 (ttp) cc_final: 0.4553 (ttt) REVERT: E 104 ASN cc_start: 0.8103 (t0) cc_final: 0.7716 (t0) REVERT: E 174 ILE cc_start: 0.8047 (mm) cc_final: 0.7841 (mm) REVERT: H 46 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6019 (mmmm) REVERT: H 66 SER cc_start: 0.7174 (p) cc_final: 0.6410 (m) REVERT: H 83 TYR cc_start: 0.6849 (m-10) cc_final: 0.6378 (m-10) outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.2828 time to fit residues: 179.2233 Evaluate side-chains 372 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 126 GLN A 288 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.177229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.152474 restraints weight = 21904.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.156939 restraints weight = 11199.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.159983 restraints weight = 7034.315| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16600 Z= 0.186 Angle : 0.653 9.547 22509 Z= 0.340 Chirality : 0.045 0.244 2551 Planarity : 0.005 0.114 2816 Dihedral : 4.768 31.775 2181 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 2.03 % Allowed : 11.03 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1947 helix: 1.58 (0.17), residues: 940 sheet: -0.70 (0.28), residues: 339 loop : -2.09 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 PHE 0.039 0.002 PHE C 301 TYR 0.023 0.002 TYR E 236 ARG 0.005 0.001 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 945) hydrogen bonds : angle 4.98850 ( 2727) SS BOND : bond 0.00263 ( 2) SS BOND : angle 2.09982 ( 4) covalent geometry : bond 0.00434 (16598) covalent geometry : angle 0.65268 (22505) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 403 time to evaluate : 1.781 Fit side-chains REVERT: A 174 ILE cc_start: 0.8495 (mm) cc_final: 0.8279 (mm) REVERT: A 186 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5804 (mm-30) REVERT: A 237 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.5944 (mtm-85) REVERT: A 286 LYS cc_start: 0.7865 (tptt) cc_final: 0.6937 (tmtt) REVERT: B 96 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.7489 (ttp-170) REVERT: B 100 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7247 (mt-10) REVERT: B 155 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6950 (tpp80) REVERT: B 186 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 187 LYS cc_start: 0.7631 (tttt) cc_final: 0.7244 (tttt) REVERT: B 197 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6525 (mm-30) REVERT: B 313 MET cc_start: 0.6032 (mtp) cc_final: 0.5451 (mtp) REVERT: B 318 MET cc_start: 0.0809 (tpt) cc_final: -0.0819 (tpt) REVERT: C 75 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7666 (tpp-160) REVERT: C 291 MET cc_start: 0.7624 (tpp) cc_final: 0.7179 (tpp) REVERT: C 327 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.5069 (t80) REVERT: D 163 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7838 (mtmm) REVERT: D 294 LEU cc_start: 0.8907 (tp) cc_final: 0.8699 (tp) REVERT: D 318 MET cc_start: 0.5702 (ttp) cc_final: 0.4587 (ttt) REVERT: E 104 ASN cc_start: 0.8200 (t0) cc_final: 0.7864 (t0) REVERT: E 125 GLU cc_start: 0.7724 (tt0) cc_final: 0.7503 (tt0) REVERT: E 162 ARG cc_start: 0.6963 (tpt90) cc_final: 0.6633 (tpt90) REVERT: E 174 ILE cc_start: 0.7972 (mm) cc_final: 0.7721 (mm) REVERT: H 46 LYS cc_start: 0.6814 (mmmt) cc_final: 0.6417 (mmmm) REVERT: H 66 SER cc_start: 0.7243 (p) cc_final: 0.6548 (m) outliers start: 37 outliers final: 30 residues processed: 416 average time/residue: 0.2811 time to fit residues: 174.9870 Evaluate side-chains 415 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 384 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 192 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN D 95 GLN D 288 ASN L 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.174339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.150275 restraints weight = 21774.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154386 restraints weight = 11642.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.157209 restraints weight = 7529.434| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16600 Z= 0.189 Angle : 0.647 8.849 22509 Z= 0.335 Chirality : 0.045 0.246 2551 Planarity : 0.005 0.115 2816 Dihedral : 4.738 32.454 2181 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.01 % Favored : 93.73 % Rotamer: Outliers : 2.63 % Allowed : 16.40 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1947 helix: 1.65 (0.17), residues: 933 sheet: -0.67 (0.28), residues: 342 loop : -2.11 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 PHE 0.025 0.002 PHE E 306 TYR 0.020 0.002 TYR E 236 ARG 0.010 0.001 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 945) hydrogen bonds : angle 4.86734 ( 2727) SS BOND : bond 0.00485 ( 2) SS BOND : angle 1.74301 ( 4) covalent geometry : bond 0.00448 (16598) covalent geometry : angle 0.64696 (22505) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 404 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.6579 (mtm) cc_final: 0.6322 (mtm) REVERT: A 174 ILE cc_start: 0.8434 (mm) cc_final: 0.8213 (mm) REVERT: A 186 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5601 (mm-30) REVERT: A 190 ASP cc_start: 0.7634 (m-30) cc_final: 0.7193 (m-30) REVERT: A 237 ARG cc_start: 0.6287 (mmm-85) cc_final: 0.5956 (mtm-85) REVERT: A 247 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7988 (m) REVERT: A 286 LYS cc_start: 0.7963 (tptt) cc_final: 0.7044 (tmtt) REVERT: A 311 TYR cc_start: 0.7437 (m-80) cc_final: 0.7209 (m-80) REVERT: B 96 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.7561 (ttp-170) REVERT: B 125 GLU cc_start: 0.6805 (tt0) cc_final: 0.6584 (tt0) REVERT: B 155 ARG cc_start: 0.7408 (mmm160) cc_final: 0.6957 (tpp80) REVERT: B 186 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6868 (tm-30) REVERT: B 187 LYS cc_start: 0.7610 (tttt) cc_final: 0.7243 (tttt) REVERT: B 197 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 275 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7208 (mm) REVERT: B 313 MET cc_start: 0.6471 (mtp) cc_final: 0.6097 (mtp) REVERT: B 318 MET cc_start: 0.0315 (tpt) cc_final: -0.1291 (tpt) REVERT: C 134 ASN cc_start: 0.8465 (p0) cc_final: 0.7849 (p0) REVERT: C 225 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8620 (tt) REVERT: C 291 MET cc_start: 0.7946 (tpp) cc_final: 0.7555 (tpp) REVERT: C 327 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.5015 (t80) REVERT: D 23 TYR cc_start: 0.7971 (m-80) cc_final: 0.7277 (m-80) REVERT: D 163 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7819 (mtmm) REVERT: D 318 MET cc_start: 0.5678 (ttp) cc_final: 0.4727 (ttt) REVERT: E 146 VAL cc_start: 0.8342 (m) cc_final: 0.7945 (p) REVERT: E 252 ARG cc_start: 0.7475 (mtp85) cc_final: 0.6935 (ttm-80) REVERT: E 313 MET cc_start: 0.5337 (tpp) cc_final: 0.4831 (tpp) REVERT: H 46 LYS cc_start: 0.6605 (mmmt) cc_final: 0.6168 (mmmm) REVERT: H 66 SER cc_start: 0.7193 (p) cc_final: 0.6521 (m) REVERT: L 2 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7616 (t0) outliers start: 48 outliers final: 34 residues processed: 419 average time/residue: 0.2627 time to fit residues: 164.6657 Evaluate side-chains 419 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 380 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 51 optimal weight: 0.3980 chunk 171 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.175446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.151421 restraints weight = 21747.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.155548 restraints weight = 11728.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.158314 restraints weight = 7611.919| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16600 Z= 0.152 Angle : 0.617 8.855 22509 Z= 0.318 Chirality : 0.044 0.242 2551 Planarity : 0.005 0.115 2816 Dihedral : 4.659 32.896 2181 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.04 % Rotamer: Outliers : 3.29 % Allowed : 17.94 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1947 helix: 1.72 (0.17), residues: 939 sheet: -0.63 (0.28), residues: 346 loop : -2.09 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 PHE 0.024 0.002 PHE E 306 TYR 0.022 0.001 TYR D 23 ARG 0.009 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 945) hydrogen bonds : angle 4.72647 ( 2727) SS BOND : bond 0.00415 ( 2) SS BOND : angle 1.43861 ( 4) covalent geometry : bond 0.00356 (16598) covalent geometry : angle 0.61711 (22505) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 398 time to evaluate : 1.717 Fit side-chains REVERT: A 28 GLU cc_start: 0.7282 (tp30) cc_final: 0.7079 (tp30) REVERT: A 174 ILE cc_start: 0.8391 (mm) cc_final: 0.8111 (mm) REVERT: A 186 GLU cc_start: 0.6299 (mm-30) cc_final: 0.5617 (mm-30) REVERT: A 190 ASP cc_start: 0.7622 (m-30) cc_final: 0.7172 (m-30) REVERT: A 237 ARG cc_start: 0.6271 (mmm-85) cc_final: 0.5979 (mtm-85) REVERT: A 247 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7958 (m) REVERT: A 286 LYS cc_start: 0.7971 (tptt) cc_final: 0.7038 (tmtt) REVERT: A 311 TYR cc_start: 0.7421 (m-80) cc_final: 0.7180 (m-80) REVERT: B 96 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7434 (ttm170) REVERT: B 154 ILE cc_start: 0.8301 (mt) cc_final: 0.8051 (mt) REVERT: B 155 ARG cc_start: 0.7382 (mmm160) cc_final: 0.6931 (tpp80) REVERT: B 163 LYS cc_start: 0.7676 (mttm) cc_final: 0.7366 (mttm) REVERT: B 186 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6799 (tm-30) REVERT: B 187 LYS cc_start: 0.7661 (tttt) cc_final: 0.7285 (tttt) REVERT: B 197 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6526 (mm-30) REVERT: B 275 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7096 (mm) REVERT: B 289 GLU cc_start: 0.7220 (tp30) cc_final: 0.7016 (tp30) REVERT: B 313 MET cc_start: 0.6448 (mtp) cc_final: 0.6213 (mtp) REVERT: B 318 MET cc_start: 0.0312 (tpt) cc_final: -0.1374 (tpt) REVERT: C 22 LYS cc_start: 0.7749 (pttm) cc_final: 0.7400 (pttp) REVERT: C 23 TYR cc_start: 0.6803 (m-80) cc_final: 0.6232 (m-10) REVERT: C 225 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8569 (tt) REVERT: C 244 GLU cc_start: 0.7635 (mp0) cc_final: 0.7391 (mp0) REVERT: C 291 MET cc_start: 0.7923 (tpp) cc_final: 0.7512 (tpp) REVERT: C 318 MET cc_start: 0.3549 (mmm) cc_final: 0.3181 (mmm) REVERT: C 327 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.4951 (t80) REVERT: D 23 TYR cc_start: 0.7937 (m-80) cc_final: 0.7310 (m-80) REVERT: D 87 LEU cc_start: 0.8501 (mt) cc_final: 0.8255 (mp) REVERT: D 134 ASN cc_start: 0.8035 (t0) cc_final: 0.7827 (t0) REVERT: D 163 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7793 (mtmm) REVERT: D 181 TYR cc_start: 0.8529 (m-80) cc_final: 0.8151 (m-80) REVERT: D 318 MET cc_start: 0.5666 (ttp) cc_final: 0.4799 (ttt) REVERT: E 131 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6877 (tt) REVERT: E 174 ILE cc_start: 0.7996 (mm) cc_final: 0.7704 (mm) REVERT: E 177 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8559 (mm) REVERT: E 252 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6805 (ttm-80) REVERT: E 313 MET cc_start: 0.5380 (tpp) cc_final: 0.4793 (tpp) REVERT: H 46 LYS cc_start: 0.6550 (mmmt) cc_final: 0.6107 (mmmm) REVERT: H 66 SER cc_start: 0.7107 (p) cc_final: 0.6387 (m) REVERT: L 2 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7621 (t0) outliers start: 60 outliers final: 38 residues processed: 424 average time/residue: 0.2730 time to fit residues: 171.6890 Evaluate side-chains 429 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 384 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 0.0470 chunk 28 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.176931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.152650 restraints weight = 22071.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.156842 restraints weight = 11853.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.159668 restraints weight = 7696.764| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16600 Z= 0.136 Angle : 0.613 9.561 22509 Z= 0.314 Chirality : 0.044 0.282 2551 Planarity : 0.005 0.116 2816 Dihedral : 4.609 32.525 2181 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.70 % Favored : 94.04 % Rotamer: Outliers : 3.40 % Allowed : 19.09 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1947 helix: 1.83 (0.17), residues: 939 sheet: -0.61 (0.28), residues: 348 loop : -2.12 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 PHE 0.023 0.001 PHE E 306 TYR 0.018 0.001 TYR D 23 ARG 0.008 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 945) hydrogen bonds : angle 4.63353 ( 2727) SS BOND : bond 0.00454 ( 2) SS BOND : angle 1.29390 ( 4) covalent geometry : bond 0.00314 (16598) covalent geometry : angle 0.61308 (22505) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 1.804 Fit side-chains REVERT: A 28 GLU cc_start: 0.7266 (tp30) cc_final: 0.7055 (tp30) REVERT: A 174 ILE cc_start: 0.8178 (mm) cc_final: 0.7844 (mm) REVERT: A 186 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5675 (mm-30) REVERT: A 237 ARG cc_start: 0.6279 (mmm-85) cc_final: 0.5980 (mtm-85) REVERT: A 247 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7916 (m) REVERT: A 286 LYS cc_start: 0.7961 (tptt) cc_final: 0.7034 (tmtt) REVERT: A 311 TYR cc_start: 0.7452 (m-80) cc_final: 0.7177 (m-80) REVERT: B 96 ARG cc_start: 0.8339 (ttp-110) cc_final: 0.7292 (ttm170) REVERT: B 154 ILE cc_start: 0.8195 (mt) cc_final: 0.7981 (mt) REVERT: B 155 ARG cc_start: 0.7339 (mmm160) cc_final: 0.6911 (tpp80) REVERT: B 163 LYS cc_start: 0.7678 (mttm) cc_final: 0.7367 (mttm) REVERT: B 186 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 187 LYS cc_start: 0.7623 (tttt) cc_final: 0.7250 (tttt) REVERT: B 197 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6426 (mm-30) REVERT: B 275 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7073 (mm) REVERT: B 313 MET cc_start: 0.6403 (mtp) cc_final: 0.6173 (mtp) REVERT: B 318 MET cc_start: 0.0397 (tpt) cc_final: -0.1291 (tpt) REVERT: C 22 LYS cc_start: 0.7794 (pttm) cc_final: 0.7415 (pttp) REVERT: C 23 TYR cc_start: 0.6773 (m-80) cc_final: 0.6182 (m-10) REVERT: C 190 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: C 225 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8535 (tt) REVERT: C 232 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7900 (mm) REVERT: C 244 GLU cc_start: 0.7601 (mp0) cc_final: 0.7338 (mp0) REVERT: C 291 MET cc_start: 0.7865 (tpp) cc_final: 0.7374 (tpp) REVERT: C 302 MET cc_start: 0.7235 (mmp) cc_final: 0.6877 (mmt) REVERT: C 318 MET cc_start: 0.3626 (mmm) cc_final: 0.3159 (mmm) REVERT: C 327 TYR cc_start: 0.5594 (OUTLIER) cc_final: 0.4887 (t80) REVERT: D 98 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7347 (pttt) REVERT: D 121 GLU cc_start: 0.7000 (pm20) cc_final: 0.6514 (pm20) REVERT: D 163 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7772 (mtmt) REVERT: D 181 TYR cc_start: 0.8584 (m-80) cc_final: 0.8270 (m-80) REVERT: D 184 LEU cc_start: 0.8694 (tt) cc_final: 0.8485 (tt) REVERT: D 318 MET cc_start: 0.5655 (ttp) cc_final: 0.4876 (ttt) REVERT: E 51 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6869 (mm) REVERT: E 174 ILE cc_start: 0.8003 (mm) cc_final: 0.7734 (mm) REVERT: E 177 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8569 (mm) REVERT: E 252 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6849 (ttm-80) REVERT: H 46 LYS cc_start: 0.6625 (mmmt) cc_final: 0.6190 (mmmm) REVERT: H 66 SER cc_start: 0.7044 (p) cc_final: 0.6314 (m) REVERT: H 114 TYR cc_start: 0.8769 (t80) cc_final: 0.8418 (t80) REVERT: H 117 TYR cc_start: 0.8904 (m-80) cc_final: 0.8529 (m-80) REVERT: L 2 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7664 (t0) REVERT: L 92 SER cc_start: 0.8864 (t) cc_final: 0.8511 (t) outliers start: 62 outliers final: 43 residues processed: 433 average time/residue: 0.2679 time to fit residues: 173.9103 Evaluate side-chains 438 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 189 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN E 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.174853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.149796 restraints weight = 21970.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.154006 restraints weight = 11897.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.156887 restraints weight = 7793.196| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16600 Z= 0.177 Angle : 0.635 8.824 22509 Z= 0.327 Chirality : 0.045 0.261 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.637 33.172 2181 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.32 % Favored : 93.43 % Rotamer: Outliers : 4.17 % Allowed : 19.75 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1947 helix: 1.77 (0.17), residues: 938 sheet: -0.53 (0.29), residues: 343 loop : -2.10 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 PHE 0.022 0.002 PHE E 306 TYR 0.017 0.002 TYR B 327 ARG 0.006 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 945) hydrogen bonds : angle 4.66068 ( 2727) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.33247 ( 4) covalent geometry : bond 0.00420 (16598) covalent geometry : angle 0.63459 (22505) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 397 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7293 (tp30) cc_final: 0.7082 (tp30) REVERT: A 186 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5712 (mm-30) REVERT: A 237 ARG cc_start: 0.6258 (mmm-85) cc_final: 0.5950 (mtm-85) REVERT: A 247 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8074 (m) REVERT: A 286 LYS cc_start: 0.8003 (tptt) cc_final: 0.7090 (tmtt) REVERT: A 311 TYR cc_start: 0.7608 (m-80) cc_final: 0.7331 (m-80) REVERT: B 24 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7635 (mmt90) REVERT: B 40 ARG cc_start: 0.6013 (ptp90) cc_final: 0.5748 (ptt-90) REVERT: B 96 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.7385 (ttm170) REVERT: B 133 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7504 (ttmt) REVERT: B 155 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6932 (tpp80) REVERT: B 163 LYS cc_start: 0.7621 (mttm) cc_final: 0.7303 (mttm) REVERT: B 186 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7122 (tm-30) REVERT: B 197 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6487 (mm-30) REVERT: B 275 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7126 (mm) REVERT: B 313 MET cc_start: 0.6311 (mtp) cc_final: 0.6109 (mtp) REVERT: B 318 MET cc_start: 0.0488 (tpt) cc_final: -0.1237 (tpt) REVERT: C 23 TYR cc_start: 0.6857 (m-80) cc_final: 0.6413 (m-10) REVERT: C 206 GLU cc_start: 0.6814 (pt0) cc_final: 0.6509 (mp0) REVERT: C 225 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8610 (tt) REVERT: C 232 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 291 MET cc_start: 0.7917 (tpp) cc_final: 0.7401 (mmt) REVERT: C 318 MET cc_start: 0.3585 (mmm) cc_final: 0.3240 (mmm) REVERT: C 327 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.4910 (t80) REVERT: D 121 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: D 163 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7780 (mtmt) REVERT: D 318 MET cc_start: 0.5653 (ttp) cc_final: 0.4862 (ttt) REVERT: E 6 LEU cc_start: 0.7232 (pt) cc_final: 0.6923 (pt) REVERT: E 51 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6942 (mm) REVERT: E 90 ILE cc_start: 0.8189 (mm) cc_final: 0.7951 (mm) REVERT: E 174 ILE cc_start: 0.8110 (mm) cc_final: 0.7858 (mm) REVERT: E 177 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8546 (mm) REVERT: E 252 ARG cc_start: 0.7364 (mtp85) cc_final: 0.6889 (ttm-80) REVERT: E 313 MET cc_start: 0.5414 (tpp) cc_final: 0.4917 (tpp) REVERT: H 46 LYS cc_start: 0.6572 (mmmt) cc_final: 0.6143 (mmmm) REVERT: H 66 SER cc_start: 0.7212 (p) cc_final: 0.6520 (m) REVERT: H 117 TYR cc_start: 0.9025 (m-80) cc_final: 0.8536 (m-80) REVERT: L 2 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7773 (t0) REVERT: L 75 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8240 (m) outliers start: 76 outliers final: 54 residues processed: 431 average time/residue: 0.2630 time to fit residues: 170.3992 Evaluate side-chains 451 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 387 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 114 optimal weight: 0.0980 chunk 148 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN D 95 GLN D 134 ASN L 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.174803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149816 restraints weight = 21975.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.154035 restraints weight = 11844.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.156899 restraints weight = 7716.453| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16600 Z= 0.165 Angle : 0.637 13.053 22509 Z= 0.326 Chirality : 0.045 0.244 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.656 32.923 2181 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 4.83 % Allowed : 19.69 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1947 helix: 1.79 (0.17), residues: 939 sheet: -0.61 (0.29), residues: 341 loop : -2.09 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 PHE 0.022 0.002 PHE E 306 TYR 0.023 0.001 TYR C 19 ARG 0.007 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 945) hydrogen bonds : angle 4.65175 ( 2727) SS BOND : bond 0.00142 ( 2) SS BOND : angle 2.71708 ( 4) covalent geometry : bond 0.00392 (16598) covalent geometry : angle 0.63645 (22505) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 1.671 Fit side-chains REVERT: A 28 GLU cc_start: 0.7275 (tp30) cc_final: 0.7062 (tp30) REVERT: A 186 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5730 (mm-30) REVERT: A 237 ARG cc_start: 0.6194 (mmm-85) cc_final: 0.5937 (mtm-85) REVERT: A 247 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8059 (m) REVERT: A 286 LYS cc_start: 0.8035 (tptt) cc_final: 0.7131 (tmtt) REVERT: A 311 TYR cc_start: 0.7472 (m-80) cc_final: 0.7222 (m-80) REVERT: B 40 ARG cc_start: 0.5986 (ptp90) cc_final: 0.5752 (ptt-90) REVERT: B 96 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7349 (ttm170) REVERT: B 100 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 133 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7505 (ttmt) REVERT: B 155 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6937 (tpp80) REVERT: B 163 LYS cc_start: 0.7615 (mttm) cc_final: 0.7294 (mttm) REVERT: B 186 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6769 (tm-30) REVERT: B 187 LYS cc_start: 0.7559 (tttt) cc_final: 0.6953 (tttt) REVERT: B 197 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6499 (mm-30) REVERT: B 275 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7416 (mm) REVERT: B 313 MET cc_start: 0.6365 (mtp) cc_final: 0.6133 (mtp) REVERT: B 318 MET cc_start: 0.0484 (tpt) cc_final: -0.1265 (tpt) REVERT: C 19 TYR cc_start: 0.8453 (t80) cc_final: 0.8203 (t80) REVERT: C 23 TYR cc_start: 0.6648 (m-80) cc_final: 0.6229 (m-10) REVERT: C 26 ASP cc_start: 0.7584 (p0) cc_final: 0.7212 (p0) REVERT: C 225 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 232 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8198 (mm) REVERT: C 291 MET cc_start: 0.7991 (tpp) cc_final: 0.7431 (mmt) REVERT: C 318 MET cc_start: 0.3501 (mmm) cc_final: 0.3238 (mmm) REVERT: C 327 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.4907 (t80) REVERT: D 42 PHE cc_start: 0.7694 (t80) cc_final: 0.7274 (t80) REVERT: D 121 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: D 134 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7390 (t0) REVERT: D 142 LYS cc_start: 0.8297 (pttt) cc_final: 0.8086 (pttt) REVERT: D 163 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7761 (mtmt) REVERT: D 181 TYR cc_start: 0.8522 (m-80) cc_final: 0.8085 (m-80) REVERT: D 291 MET cc_start: 0.7908 (tpp) cc_final: 0.7581 (tpp) REVERT: D 318 MET cc_start: 0.5649 (ttp) cc_final: 0.5153 (ttt) REVERT: E 6 LEU cc_start: 0.6998 (pt) cc_final: 0.6681 (pt) REVERT: E 51 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6882 (mm) REVERT: E 90 ILE cc_start: 0.8152 (mm) cc_final: 0.7918 (mm) REVERT: E 177 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 252 ARG cc_start: 0.7355 (mtp85) cc_final: 0.6967 (ttm-80) REVERT: E 313 MET cc_start: 0.5525 (tpp) cc_final: 0.4980 (tpp) REVERT: H 46 LYS cc_start: 0.6573 (mmmt) cc_final: 0.6130 (mmmm) REVERT: H 66 SER cc_start: 0.7198 (p) cc_final: 0.6510 (m) REVERT: H 117 TYR cc_start: 0.9041 (m-80) cc_final: 0.8596 (m-80) REVERT: L 2 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7677 (t0) REVERT: L 75 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8244 (m) outliers start: 88 outliers final: 63 residues processed: 435 average time/residue: 0.2679 time to fit residues: 175.4616 Evaluate side-chains 458 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 384 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 148 optimal weight: 0.8980 chunk 149 optimal weight: 0.2980 chunk 133 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.175452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150434 restraints weight = 21776.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.154672 restraints weight = 11792.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.157545 restraints weight = 7700.256| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16600 Z= 0.157 Angle : 0.652 12.598 22509 Z= 0.330 Chirality : 0.045 0.243 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.641 32.762 2181 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.11 % Favored : 93.68 % Rotamer: Outliers : 4.50 % Allowed : 20.08 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1947 helix: 1.81 (0.17), residues: 939 sheet: -0.57 (0.29), residues: 342 loop : -2.07 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 PHE 0.021 0.002 PHE E 306 TYR 0.020 0.001 TYR C 19 ARG 0.006 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 945) hydrogen bonds : angle 4.63393 ( 2727) SS BOND : bond 0.00537 ( 2) SS BOND : angle 2.51710 ( 4) covalent geometry : bond 0.00372 (16598) covalent geometry : angle 0.65072 (22505) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 397 time to evaluate : 1.848 Fit side-chains REVERT: A 186 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5719 (mm-30) REVERT: A 237 ARG cc_start: 0.6171 (mmm-85) cc_final: 0.5922 (mtm-85) REVERT: A 247 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8145 (m) REVERT: A 286 LYS cc_start: 0.8033 (tptt) cc_final: 0.7150 (tmtt) REVERT: A 311 TYR cc_start: 0.7499 (m-80) cc_final: 0.7101 (m-80) REVERT: B 40 ARG cc_start: 0.5964 (ptp90) cc_final: 0.5728 (ptt-90) REVERT: B 96 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.7348 (ttm170) REVERT: B 100 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6861 (mt-10) REVERT: B 155 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6926 (tpp80) REVERT: B 163 LYS cc_start: 0.7634 (mttm) cc_final: 0.7310 (mttm) REVERT: B 186 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6810 (tm-30) REVERT: B 187 LYS cc_start: 0.7516 (tttt) cc_final: 0.7026 (ttpt) REVERT: B 197 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6516 (mm-30) REVERT: B 275 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7404 (mm) REVERT: B 318 MET cc_start: 0.0622 (tpt) cc_final: -0.1093 (tpt) REVERT: C 23 TYR cc_start: 0.6701 (m-80) cc_final: 0.6285 (m-10) REVERT: C 26 ASP cc_start: 0.7596 (p0) cc_final: 0.7286 (p0) REVERT: C 225 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 232 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 263 ASP cc_start: 0.7462 (m-30) cc_final: 0.7019 (m-30) REVERT: C 291 MET cc_start: 0.8107 (tpp) cc_final: 0.7891 (tpp) REVERT: C 318 MET cc_start: 0.3467 (mmm) cc_final: 0.3215 (mmm) REVERT: C 327 TYR cc_start: 0.5625 (OUTLIER) cc_final: 0.4859 (t80) REVERT: D 42 PHE cc_start: 0.7665 (t80) cc_final: 0.7202 (t80) REVERT: D 121 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: D 142 LYS cc_start: 0.8309 (pttt) cc_final: 0.8089 (pttt) REVERT: D 163 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7758 (mtmm) REVERT: D 181 TYR cc_start: 0.8538 (m-80) cc_final: 0.8088 (m-80) REVERT: D 318 MET cc_start: 0.5644 (ttp) cc_final: 0.5135 (ttt) REVERT: E 6 LEU cc_start: 0.6966 (pt) cc_final: 0.6679 (pt) REVERT: E 51 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6868 (mm) REVERT: E 90 ILE cc_start: 0.8166 (mm) cc_final: 0.7925 (mm) REVERT: E 162 ARG cc_start: 0.7295 (tpt90) cc_final: 0.7065 (tpt90) REVERT: E 177 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8586 (mm) REVERT: E 252 ARG cc_start: 0.7345 (mtp85) cc_final: 0.6967 (ttm-80) REVERT: H 66 SER cc_start: 0.7153 (p) cc_final: 0.6460 (m) REVERT: H 117 TYR cc_start: 0.9036 (m-80) cc_final: 0.8628 (m-80) REVERT: L 2 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7700 (t0) REVERT: L 75 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8235 (m) outliers start: 82 outliers final: 67 residues processed: 432 average time/residue: 0.2650 time to fit residues: 173.4019 Evaluate side-chains 464 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 387 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 15 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.173584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.148559 restraints weight = 21902.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.152752 restraints weight = 11865.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.155597 restraints weight = 7787.548| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16600 Z= 0.182 Angle : 0.669 12.351 22509 Z= 0.340 Chirality : 0.046 0.246 2551 Planarity : 0.005 0.118 2816 Dihedral : 4.673 32.963 2181 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.52 % Favored : 93.22 % Rotamer: Outliers : 4.72 % Allowed : 20.52 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1947 helix: 1.73 (0.17), residues: 939 sheet: -0.54 (0.29), residues: 337 loop : -2.09 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 PHE 0.020 0.002 PHE E 306 TYR 0.045 0.002 TYR C 19 ARG 0.006 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 945) hydrogen bonds : angle 4.67628 ( 2727) SS BOND : bond 0.00440 ( 2) SS BOND : angle 2.46643 ( 4) covalent geometry : bond 0.00433 (16598) covalent geometry : angle 0.66801 (22505) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 400 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6827 (t80) cc_final: 0.6227 (t80) REVERT: A 186 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5702 (mm-30) REVERT: A 237 ARG cc_start: 0.6153 (mmm-85) cc_final: 0.5894 (mtm-85) REVERT: A 247 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 286 LYS cc_start: 0.8064 (tptt) cc_final: 0.7170 (tmtt) REVERT: B 96 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7348 (ttm170) REVERT: B 155 ARG cc_start: 0.7355 (mmm160) cc_final: 0.6951 (tpp80) REVERT: B 163 LYS cc_start: 0.7633 (mttm) cc_final: 0.7312 (mttm) REVERT: B 186 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 187 LYS cc_start: 0.7476 (tttt) cc_final: 0.6983 (ttpt) REVERT: B 227 PRO cc_start: 0.9052 (Cg_exo) cc_final: 0.8711 (Cg_endo) REVERT: B 275 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 313 MET cc_start: 0.5923 (mtp) cc_final: 0.5521 (mtp) REVERT: B 318 MET cc_start: 0.0679 (tpt) cc_final: -0.1055 (tpt) REVERT: C 26 ASP cc_start: 0.7565 (p0) cc_final: 0.6992 (p0) REVERT: C 225 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8656 (tt) REVERT: C 232 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8289 (mm) REVERT: C 263 ASP cc_start: 0.7496 (m-30) cc_final: 0.7106 (m-30) REVERT: C 327 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.4821 (t80) REVERT: D 42 PHE cc_start: 0.7621 (t80) cc_final: 0.7237 (t80) REVERT: D 121 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: D 142 LYS cc_start: 0.8363 (pttt) cc_final: 0.8107 (pttt) REVERT: D 163 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7683 (mtmm) REVERT: D 246 GLU cc_start: 0.7013 (tt0) cc_final: 0.6754 (tt0) REVERT: D 318 MET cc_start: 0.5689 (ttp) cc_final: 0.5198 (ttt) REVERT: E 6 LEU cc_start: 0.6966 (pt) cc_final: 0.6676 (pt) REVERT: E 51 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6959 (mm) REVERT: E 90 ILE cc_start: 0.8216 (mm) cc_final: 0.7974 (mm) REVERT: E 177 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8620 (mm) REVERT: E 204 GLU cc_start: 0.7320 (tt0) cc_final: 0.7018 (tt0) REVERT: E 252 ARG cc_start: 0.7349 (mtp85) cc_final: 0.6969 (ttm-80) REVERT: H 66 SER cc_start: 0.7255 (p) cc_final: 0.6584 (m) REVERT: H 117 TYR cc_start: 0.9049 (m-80) cc_final: 0.8703 (m-80) REVERT: L 2 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (t0) REVERT: L 75 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8247 (m) outliers start: 86 outliers final: 69 residues processed: 439 average time/residue: 0.2836 time to fit residues: 186.7911 Evaluate side-chains 471 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 392 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 63 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 137 optimal weight: 0.0670 chunk 144 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.175665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.150584 restraints weight = 22061.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.154883 restraints weight = 11891.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.157773 restraints weight = 7760.720| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16600 Z= 0.146 Angle : 0.655 12.102 22509 Z= 0.332 Chirality : 0.045 0.250 2551 Planarity : 0.005 0.118 2816 Dihedral : 4.630 32.165 2181 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer: Outliers : 4.22 % Allowed : 21.23 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1947 helix: 1.86 (0.17), residues: 937 sheet: -0.60 (0.28), residues: 347 loop : -2.10 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 PHE 0.021 0.001 PHE E 306 TYR 0.016 0.001 TYR D 23 ARG 0.007 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 945) hydrogen bonds : angle 4.62518 ( 2727) SS BOND : bond 0.00492 ( 2) SS BOND : angle 2.55052 ( 4) covalent geometry : bond 0.00342 (16598) covalent geometry : angle 0.65443 (22505) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 396 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7178 (tp30) cc_final: 0.6877 (tp30) REVERT: A 96 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8256 (ptm-80) REVERT: A 97 PRO cc_start: 0.8823 (Cg_exo) cc_final: 0.8545 (Cg_endo) REVERT: A 186 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5904 (mm-30) REVERT: A 237 ARG cc_start: 0.6126 (mmm-85) cc_final: 0.5822 (mtm-85) REVERT: A 247 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 286 LYS cc_start: 0.8048 (tptt) cc_final: 0.7166 (tmtt) REVERT: B 26 ASP cc_start: 0.6450 (t0) cc_final: 0.6085 (t0) REVERT: B 96 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7321 (ttm170) REVERT: B 100 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6815 (mt-10) REVERT: B 155 ARG cc_start: 0.7337 (mmm160) cc_final: 0.6926 (tpp80) REVERT: B 163 LYS cc_start: 0.7615 (mttm) cc_final: 0.7281 (mttm) REVERT: B 186 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6793 (tm-30) REVERT: B 187 LYS cc_start: 0.7496 (tttt) cc_final: 0.7024 (ttpt) REVERT: B 197 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6436 (mm-30) REVERT: B 275 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7357 (mm) REVERT: B 313 MET cc_start: 0.5592 (mtp) cc_final: 0.5201 (mtp) REVERT: B 318 MET cc_start: 0.0707 (tpt) cc_final: -0.0986 (tpt) REVERT: C 225 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8571 (tt) REVERT: C 232 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8063 (mm) REVERT: C 263 ASP cc_start: 0.7517 (m-30) cc_final: 0.7133 (m-30) REVERT: C 327 TYR cc_start: 0.5540 (OUTLIER) cc_final: 0.4746 (t80) REVERT: D 42 PHE cc_start: 0.7594 (t80) cc_final: 0.7280 (t80) REVERT: D 121 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6728 (pm20) REVERT: D 142 LYS cc_start: 0.8324 (pttt) cc_final: 0.8071 (pttt) REVERT: D 163 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7730 (mtmm) REVERT: D 318 MET cc_start: 0.5691 (ttp) cc_final: 0.5170 (ttt) REVERT: E 6 LEU cc_start: 0.6899 (pt) cc_final: 0.6655 (pt) REVERT: E 26 ASP cc_start: 0.7952 (t0) cc_final: 0.7644 (t70) REVERT: E 51 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6929 (mm) REVERT: E 90 ILE cc_start: 0.8134 (mm) cc_final: 0.7892 (mm) REVERT: E 177 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8594 (mm) REVERT: E 252 ARG cc_start: 0.7272 (mtp85) cc_final: 0.6872 (ttm-80) REVERT: H 66 SER cc_start: 0.7109 (p) cc_final: 0.6431 (m) REVERT: H 117 TYR cc_start: 0.9021 (m-80) cc_final: 0.8697 (m-80) REVERT: L 75 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8207 (m) outliers start: 77 outliers final: 65 residues processed: 429 average time/residue: 0.2681 time to fit residues: 171.8977 Evaluate side-chains 466 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 392 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.171963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.146941 restraints weight = 21962.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.151160 restraints weight = 11960.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.153976 restraints weight = 7852.867| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16600 Z= 0.204 Angle : 0.700 11.731 22509 Z= 0.357 Chirality : 0.047 0.247 2551 Planarity : 0.005 0.118 2816 Dihedral : 4.767 32.660 2181 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.14 % Favored : 92.55 % Rotamer: Outliers : 4.00 % Allowed : 21.72 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1947 helix: 1.67 (0.17), residues: 937 sheet: -0.57 (0.29), residues: 333 loop : -2.11 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 350 HIS 0.006 0.001 HIS C 212 PHE 0.022 0.002 PHE B 301 TYR 0.025 0.002 TYR C 19 ARG 0.008 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 945) hydrogen bonds : angle 4.74825 ( 2727) SS BOND : bond 0.00488 ( 2) SS BOND : angle 2.57829 ( 4) covalent geometry : bond 0.00488 (16598) covalent geometry : angle 0.69880 (22505) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6507.65 seconds wall clock time: 114 minutes 54.31 seconds (6894.31 seconds total)